At this time we are able to offer two services for running WDL workflows on Google Cloud using the Cromwell execution engine and the Google Pipelines API. Note that while access to both of these services is free, compute and storage are subject to Google Cloud pricing, charged directly by Google (Broad does not apply any markup).
Terra: Our secure, freely accessible cloud-based analysis portal
This web-based application is provided as a freely accessible service by the Broad Institute's Data Sciences Platform, where GATK itself is also developed. Terra (formerly FireCloud) provides both GUI (point-and-click) and API access to a persistent Cromwell execution server that manages submissions to the Google Pipelines API. In addition to the core pipeline execution service, the Terra platform also includes functionality for data management, a data library of published datasets (including TCGA data) and a method repository for managing and sharing workflows. The platform as a whole is designed to empower analysts, tool developers and production managers to perform large-scale analysis, engage in data curation, and store or publish results. You can find out more about how Terra can make it easier for you to run GATK Best Practices pipelines here.
WDL and Cromwell
Our Best Practices workflow scripts are publicly available within the gatk-workflows GitHub repository. Furthermore, we provide Docker containers for all versions of GATK in DockerHub. See the Best Practices to browse the pipelines by use case. Our open-source workflows are written in WDL, and take advantage of Cromwell's flexibility in being able to run on a variety of different platforms, both local and cloud-based.
See our Pipelining GATK with WDL and Cromwell article for more information.
For even more information, check out Genomics in the Cloud, which is a book that goes deep into using Docker, GATK, and WDL in Terra.
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